Echinococcus granulosus sensu lato is the causative agent of cystic echinococcosis (CE), a globally distributed zoonotic infection. In Guatemala, no new data have been reported for the past 80 years on CE. To address this gap, a cross-sectional study at the municipal slaughterhouse of Quetzaltenango was conducted from March to August 2022 to determine the presence of Echinococcus sp. in backyard pigs. Moreover, the species and haplotypes, fertility status of hydatid cysts, association of fertility of the cysts to the sex of the pig and the size of cysts were investigated. For this purpose, 117 pigs were examined post-mortem, and cysts were extracted from their organs. Species identification was performed using nested polymerase chain reaction targeting the cox1 gene, and a haplotype network was constructed. Generalized linear models (GLMs) were applied to assess correlation between cysts fertility, sex of the pig and diameter of the cyst. The study revealed a high prevalence of 38·46% of CE, and a minimum prevalence of Taenia hydatigena of 4·27%. Genetic characterization confirmed the presence of Echinococcus canadensis of the G7 haplogroup. Eight haplotypes unique to Guatemala were identified, along with one of global occurrence. Cysts from male pigs were 3·6 times more likely to be fertile than those from female pigs. A quadratic GLM determined that cysts with a diameter range of 2·09–4·20 cm had a higher probability of being fertile. The high prevalence of CE and the diversity of Guatemalan haplotypes confirm the endemicity of E. canadensis in this region.